MAY 2014 Newsletter Volume 27, No. 2

IN THIS ISSUE Society Letter from the President ...... 2 SMB Treasurer Update - Renée Fister ...... 3 2014 JSMB/SMB Annual Meeting Announcement ...... 4 Recent Conference Reports Advances in Mathematical Biology, Colombia ...... 5 Systems Approaches in Immunology, Santa Fe, NM ...... 6 Reports from The 2014 Joint Mathematics Meetings, Baltimore, MD ...... 8 Translating Cancer Data and Models to Clinical Practice, UCLA, California ...... 9 SMB at the USA Science & Engineering Festival, Thinking Like Ants!, Washington DC ...... 11 Computational Neuroscience Workshop, McGill University, Montréal ...... 13 Perspectives "New and Less New Opportunities For Mathematical Biology as Applied To Biological and Clinical Medicine" - Jean Clairambault ...... 14 SMB Education Highlights New Guidelines for Programs in Mathematical Biology - Elsa Schaefer ...... 16 People Mathematical Biology Journey - Trachette L. Jackson ...... 18 James D. Murray Talks About His Benter Prize ...... 20 Philip Maini Interviews James D. Murray ...... 21 Research Interview - Nick Cogan ...... 22 The Future of Mathematical Biology - Russ Rockne ...... 24 Positions Available ...... 26 Institute Events ...... 27

https://sites.google.com/site/jsmbsmbjointmeeting2014osaka/home

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 1 MAY 2014

Letter from the President

Dear SMB members,

When I was out plucking ruefully at the dandelions in our lawn the other day, I was accosted by my lawyer neighbor who was doing the same, although rather more forcefully. "What do you teach, anyway?" he asked, and I said "math and biology", which elicited the response we have all become so used to, "Those seem like two completely unrelated subjects." He seemed the wrong per- son to get into an argument with, so I attacked another dan- delion. Perhaps the Society will have succeeded when we don’t hear some such response every time we confess to what we do.

As I look through this newsletter and think about the goals of the So- ciety, it is clear that neighbors are just one of the many audiences we have a chance to educate. Schoolchil- dren, college students, academic colleagues, administrators, and medical researchers need to feel the gath- ering wave of successful education, research, and application that mark not so much an oncoming flood of mathematical biology as the filling of a waterway.

This mathematical waterway is a conduit of scientific communication. Historically, cities were founded almost invariably near waterways less for water supply and security than for efficient transportation. Even today, floating a ship, perhaps from California to Japan, takes far less energy than any other mode of trans- port because the buoyancy of the water does most of the work of fighting gravity and friction. And that is precisely the promise of mathematical biology. When the good ship math biology is sailing the intellectual oceans with cargo ranging from cancer delivery strategies and models of ant behavior to ways to combat biofilm-associated diseases, our neighbors of all sorts will know that mathematics belongs in biology be- cause it often provides the most efficient way to solve problems.

The upcoming joint meeting in Osaka with the Japanese Society for Mathematical Biology makes con- nections across geographic rather than conceptual distance. Even in the era of globalization, the rich tradi- tions of Japanese, Chinese and Korean science are something many of us in Europe and the Americas know only through published work and some lucky encounters. I am looking forward to diving more deeply into that world and expanding my network of friends, colleagues and collaborators.

Sincerely,

Fred Adler

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 2 MAY 2014

SMB Treasurer Update

Dear SMB members,

It is hard to believe that another fiscal year for SMB has come and gone. Our year runs from April 1 through March 31. Many thanks to Torcom Chor- bajian for his multiple years of service to the society and for graciously doing the taxes for 2013! He has been instrumental in keeping the society moving in the financial aspects. As of November 2012, we began a transition period in which I began to learn the ropes, if you will. With Torcom and Heiko Ender- ling’s membership support, we migrated to an online membership system with a connection to PayPal. Heiko has done a fabulous job of keeping in contact with Springer regarding the membership so that the Bulletin of Mathemat- ical Biology can be properly distributed to you, either in print or electroni- cally.

The Travel and World Outreach Committees have worked to provide opportunities for people to host workshops throughout this past year. There have been events in Buenos Aires, Columbia, and Israel, to name a few. An entire programmatic concept related to Models and Methods in Ecology, Epidemiology, and Health created opportunities for workshops throughout this last year. For each sponsored event, doc- umentation is required. A standardized SMB travel form has been developed. Each participant completes the fillable form provided by the workshop organizer or via my email, kfi[email protected]. After the workshop organizer has determined the allocation of the funds and the forms with the receipts have been received, then disbursement has been sent. Please note that if a wire transfer is requested that there is a cost associated with that which is subtracted from the reimbursement funds. For each workshop, the paperwork for all is requested to be returned within a month of the event, if at all possible. A second item related to documentation is an article that is to be sent to the SMB Newsletter concerning the workshop. If you have not done so, please send your articles to Amina Eladdadi at [email protected].

Some bookkeeping items that have occurred this past year are the use of QuickBooks for all the income and expenses of the society. We are a solid group financially to date. We are working on mechanisms to enhance the growth of our funds. There is a task force that is looking at the cost of membership for the dif- ferent categories and the benefit for our members. We have also had our Articles of Incorporation updated, and they are now current and in good standing through 2016 as required by the government.

As you are planning for our joint annual meeting hosted by the Japanese Society for Mathematical Biol- ogy in Osaka, Japan from July 28-August 1, remember to see if you are eligible for the Landahl-Busenberg awards, http://www.smb.org/meetings/landahl.shtml.

Your support of SMB has given opportunities to researchers to continue their studies in different cul- tures and interdisciplinary aspects. Thanks for your continued support!

Renée Fister, SMB Treasurer

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 3 MAY 2014

The 2014 JSMB/SMB Annual Meeting Announcement

Dear SMB members,

The joint annual meeting of the Japanese Society for Mathematical Bi- ology (JSMB) and the Society for Mathematical Biology (SMB) will take place at Osaka International Conference Center in Osaka, Japan, from July 28-August 1, 2014. The joint meetings of the SMB and the JSMB were held first at Hilo, Hawaii in 2001, and second at San Jose, Cali- fornia in 2007. This third joint meeting is the first one held in Japan, and co-sponsored by the Chinese Society for Mathematical Biology and the Korean Society for Mathematical Biology. The themes of the confer- ence will include all areas of mathematical biology at the interface of mathematics and its application to biology. Professor Masayasu Mimura (Meiji University, Tokyo), President of the JSMB, will chair the confer- ence.

The meeting will feature nine plenary lectures, by Dr. Nanako Shigesada (2013 Akira Okubo Prize Awardee, Professor Emeritus of Nara Women’s University, Japan), Carson C. Chow (NIH, USA), Dr. Iain D. Couzin (Princeton University, USA), Dr. Steve A. Frank (Univ. California at Irvine, USA), Dr. Hawoong Jeong (KAIST, Korea), Dr. Laura Miller (University of North Carolina, USA), Dr. Akiko Satake (Hokkaido University, Japan), Dr. Tatsuo Shibata (Center for Developmental Biology, RIKEN Kobe, Japan), and Dr. Yanni Xiao (Xi’an Jiaotong University, China) and two Lee Segel prize lectures.

Seventy one minisymposia (including double sessions) were proposed in the areas of Medicine, Virus, Cancer, Cell Biology, Developmental Biology, Pattern Formation, Biological Movement, Network, Epidemi- ology, Ecology, Evolution, and Mathematics from USA, Canada, UK, Germany, France, Austria, Poland, Australia, Saudi Arabia, China, Korea, Taiwan, and Japan. The number of minisymposia exceeded the total of numbers of minisymposia and contributed sessions combined at the Tempe meeting. In expectation of numerous presentations at contributed oral and poster sessions, we will be able to welcome many partici- pants from all over the world.

Summer in Osaka is very hot and humid, so although the temperature itself is much lower than that at Tempe, casual wear made of fabric that breathes well is recommended. The local organizing committee (https://sites.google.com/site/jsmbsmbjointmeeting2014osaka/organizing-committee) will make every effort to appreciate excellent presentations and productive discussion in a comfortable atmosphere.

Please visit https://sites.google.com/site/jsmbsmbjointmeeting2014osaka/home for details.

Minisymposia: https://sites.google.com/site/jsmbsmbjointmeeting2014osaka/minisymposia .

Toshiyuki Namba, On behalf of the Organizing Committees

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 4 Advances in Mathematical Biology Universidad Autónoma de Occidente, Colombia, November 20th, 2013 by PAULA GONZALEZ

Report by an SMB WOC - Grant Recipient

The workshop AMAB 2013 was held at Universi- dad Autónoma de Occidente in Cali Colombia, on November 20th, 2013. In the previous workshop (2010) we had around 30 participants, while at this time the audience reached about 50 people. There were students and professors from several univer- sities in Colombia: Universidad de Los Andes (Bo- gotá), Universidad del Quindio (Armenia), Universi- dad de Pasto (Pasto), Universidad del Valle, Univer- sidad Icesi, and Universidad Autónoma de Occidente (Cali). Group Photo These universities represented different geo- graphical regions of Colombia. Also we had re- During the workshop we had three mini-courses: searchers coming from United States, France, Korea Optimal Control, Optimization and Applications in and Guatemala. Machine Learning, and Neurocomputation. These With the SMB world Outreach support we were were offered by Professors Sunmi Lee, and David able to invite Professor Sunmi Lee from Kyung Hee Ramirez respectively. The Plenary lectures were pre- University (Korea), Dr. Reinaldo Sanchez from The sented by Professors Carlos Castillo-Chavez from University of Texas at El Paso (USA) and Profes- Arizona State University, Vladick Kreinovich from sor William Polanco from Rafael Landivar Univer- The University of Texas at El Paso and Michel De sity (Guatemala). The mission of these enthusiastic Lara from Universite Paris-Est France. young scientists was not only to offer mini-courses There were poster and oral presentations given and oral presentation, but also to motivate and en- by students and researchers from the different par- courage our students and young researcher into pur- ticipant universities from Colombia. It was a great suing further academic career in the area of mathe- opportunity for both undergraduate and graduate matical biology, which we visualize has a promising students to get constructive feedback from outstand- future in Colombia. ing researchers; in particular they had great time learning from Carlos Castillo-Chavez a well known mentor and leader in the area. For most of the stu- dents it was the first time to attend a workshop with top-notch researchers. Based on all these accom- plishments, we truly believe that our main goal, i.e. dissemination of research results among local schol- ars and seeking of possible collaboration for further research, was reached and we look forward to con- tinue working with the same commitment and pro- fessionalism. We want to thank The Society for Mathemati- cal Biology for their financial support, without it, it Carlos Castillo-Chavez, Sunmi Lee, Michel De Lara , and would have been more difficult to invite these high Reinaldo Sanchez quality researchers and reach our goals.

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 5 Systems Approaches in Immunology Santa Fe, NM, January 10-11, 2014 by VITALY GANUSOV

Report by an SMB - Grant Recipient

The third biennial conference on Systems Ap- proaches in Immunology and Infectious Diseases was held in Santa Fe, NM on January 10 - 11, 2014. As with the first two international work- shops, this meeting provided a multidisciplinary fo- rum to discuss the latest developments at the bound- ary of experimental and computational immunol- ogy. It was organized under the premise that un- derstanding of immunology will be advanced by the development of theoretical and experimental tech- niques and models that bring together phenomena at different levels of complexity. Research themes focused on systems-level analysis of immunological processes and spanned the molecular, cellular, pop- ulation, and organismal levels, both experimentally Venue of the meeting: beautiful Santa Fe and theoretically. The meeting included talks, panel discussions and a poster session. It was organized Following a short break, the next talk was given by Vitaly Ganusov (University of Tennessee), Steven by Garnett Kelsoe from the Department of Immunol- Kleinstein (Yale School of Medicine), Alan Perelson ogy at Duke University School of Medicine.This talk (LANL) and Ruy Ribeiro (LANL). The meeting was focused on the origin of natural antibodies, antibod- held under the auspices of the Center for Nonlinear ies which arise in young individuals in the absence of Studies (CNLS) of Los Alamos National Laboratory, exposure to any foreign antigen. The final talk in the with support from the Society for Mathematical Bi- session was given by Alan Perelson from Los Alamos ology and the Army Research Office. National Laboratory, who presented a model, devel- oped with Jessica Conway also from Los Alamos, to The meeting started out on Friday January 10 account for post-treatment control of HIV to unde- with a session on Systems Approaches in Humoral tectable levels using a model that exhibited bistabil- Immunity. The first two talks focused on B cell re- ity in the viral set-point of HIV. sponses in the germinal centers. Mark Shlomchik On Friday afternoon, the session theme was Sys- from the Immunology Department at the Pittsburgh tems Approaches in Cellular Immunity and the ses- School of Medicine gave a brief history of how mod- sion consisted of six contributed presentations on eling has been used to investigate B cell popula- this topic. The first four covered issues of T-cell tion dynamics and affinity maturation in the ger- homeostasis. Jose Borghans from the Immunology minal center. Next, Rob De Boer from Theoretical Department at the University Medical Center in Biology and Bioinformatics, Utrecht University pro- Utrecht, Netherlands, presented experimental and posed a mathematical model for how germinal cen- modeling work to understand the maintenance of ters evolve broadly neutralizing antibodies. Arup the lymphocyte pool during healthy ageing. Next, Chakraborty from the Department of Chemical En- Robin Callard, from the Institute of Child Health gineering, MIT continued on the theme of HIV. He at University College London, analyzed T-cell recon- presented a statistical physics approach to designing stitution in HIV-infected children under antiretro- immunogens that could be used as vaccine compo- viral therapy. Julia Drylewicz, also from Utrecht, nents. presented kinetic T-cell data from mice and hu-

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 6 mans to study whether recent thymic emigrants On the final session of the meeting (Saturday af- formed a short-lived sub-population of the naive T- ternoon) the main theme of presentations was Sys- cell compartment. Changing the subject slightly, Vi- tems Approaches in Signaling. The session stated taly Ganusov, from the University of Tennessee, pre- with a talk by Lily Chylek, from Cornell, on T cell sented detailed analyses of experiments on lympho- receptor signaling and the role of SHP-1 in enhanc- cyte recirculation, where radioactively labeled lym- ing early signaling events. Next, Jialiang Wu, from phocytes were injected in animals and then collected the Yale School of Medicine, presented a mathe- at several times. After a coffee break, Benedict Sed- matical model of interferon stimulated gene (ISG) don of the Medical Research Council in the UK pre- dynamics. The next talk by Chitra Nayak, the Uni- sented work on trying to understand CTL killing ef- versity of Toronto, also focused on the interferon ficiency from different target types, including differ- response. Rodolphe Thiebaut, INSERM, then pre- ent levels of antigen on the target. The final talk of sented experimental data from a recent trial of a the day was by Victor Garcia of the ETH in Zurich. therapeutic vaccine against HIV involving ex vivo He re-analyzed data on HIV escape from CD8+ T- generated dendritic cells loaded with HIV-derived cell recognition (timings and rates), re-interpreting lipopeptides. Daniel Gadala-Maria, from Yale School the observations in terms genetic interference (and of Medicine, presented a novel method for detection linkage) among HIV escape strains. On Friday af- of novel immunoglobulin (Ig) V segments from next- ternoon there was an informal poster session, with generation Ig sequencing data (Rep-Seq). The next a reception followed by dinner. There were about talk by Grant Lythe, University of Leeds, switched 20 posters presented, which generated much discus- gears to dynamics of T cells in the body with the sion. Indeed the posters were on display throughout question of how many different T cell specificities dinner time until the next morning, and generated can the body maintain. The session was concluded much traffic and lively conversation between the au- by the talk of Phillip Johnson, Emory University, dis- thors and the other participants. cussing the puzzle of T cell receptor repertoires in humans. The second day of the meeting, January 11, The meeting was well attended by junior scien- opened with a morning session on System Ap- tists, and five of these received travel support from proaches for Understanding Immune Responses. It the Society for Mathematical Biology. Altogether, was opened by Denise Kirschner, the University of this was a very productive meeting, in the lovely set- Michigan, who gave a thorough overview of her ting of "Inn at Loretto" in Santa Fe, which allowed work over the last decade on using multiscale and plenty of discussion among the participants. The systems approaches to uncovering the mechanisms feedback received by the organizers was in general governing immunity to tuberculosis. Her talk was very positive, with encouragement to hold a fourth followed by an exciting presentation by John Tsang installment of these meetings in January 2016. from the Laboratory of Systems Biology, NIAID and the Tarns-NIH Center on Human Immunology, dis- cussing methods for quantifying the immune re- sponse to seasonal influenza vaccination focusing on the variation in response among 63 healthy volun- teers. Matthew Krummel from the University of Cali- fornia at San Francisco then discussed his group’s in- travital imaging studies of T cell motion focusing on the theoretical question of how T cells move to max- imize surveillance for foreign material on the sur- face of antigen-presenting cells. Lastly, Joshua Schif- fer, MD from the Fred Hutchison Cancer Research Center and University of Washington in Seattle de- scribed work done over the last decade by his lab to understand the spatial-temporal aspects of human Discussions did not stop after presentations: Garnett simplex virus-2 (HSV-2) infection and immune re- Kelsoe, Alan Perelson, Arup Chakraborty, Rob De Boer, sponses in the human genital track. and Mark Schlomchik

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 7 Reports from The 2014 Joint Mathematics Meetings Baltimore, MD, January 17, 2014

Mathematics in Natural Resource Undergraduate Mathematical Modeling Biology Education by CATHERINE ROBERTS by TIM COMAR

The sessions on Mathematics in Natural Re- On Friday, January 1, the MAA Special Interest source Modeling at the Joint Mathematics Meet- Group in Mathematical and Computational Biology ing in Baltimore, MD in January 2014 included (BIO SIGMAA) sponsored the MAA Contributed Pa- a total of 16 talks and were very well-attended. per Session, Trends in Undergraduate Mathematical Further information about the talks can be Biology Education at the Joint Mathematics Meet- found here: http://jointmathematicsmeetings. ings in Baltimore. The topics of the twelve talks org/meetings/national/jmm2014/2160_program_ include discussions of Bio-calculus courses, upper ss43.html level courses, including a presentation of a course on the Mathematics of Cancer at Arizona State Univer- sity by Eric Kostelich, and undergraduate research projects. One particular highlight was Drew LaMar’s intro- duction to the currently under development Quan- titative Undergraduate Biology Education and Syn- thesis (QUBES) Hub, which will serve a central re- source for educational materials in quantitative bi- ology and a social network. As quantitative tools are recognized as more important to biologists, and bi- ological applications of more interest to mathemati- cians, an interdisciplinary approach to education in these areas is crucial. A similar session will occur at the 2015 Suzanne Lenhart : Optimal control in models of Joint Mathematics Meetings, and a contributed management of forest resources paper session focusing on undergraduate re- search projects will occur at Mathfest in 2014 in Portland, OR. Check out the website for abstracts: http://jointmathematicsmeetings. org/meetings/national/jmm2014/2160_program_ friday.html#2160:MCPCOMN5 and

Shandelle Henson: Reproductive synchrony in populations can ameliorate the effects of adult-on-juvenile cannibalism Drew LaMar giving his presentation on QUBES

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 8 Translating Cancer Data and Models to Clinical Practice University of California Los Angeles, February 10-14, 2014 by DANA-ADRIANA BOTESTEANU &GEOFFREY CLAPP

This workshop on understanding cancer dynam- cancer, given the peculiar natural history of the dis- ics from a multitude of morphological, proteomic, ease. Doron Levy (Maryland) closed the afternoon genomic and mathematical perspectives took place with a mathematical modeling presentation on the at the Institute of Pure and Applied Mathematics role of symmetric and asymmetric division of stem (IPAM) at the University of California Los Angeles cells in developing drug resistance to cancer, using (UCLA) from February 10-14, 2014. The workshop ordinary differential equations. A poster session and was organized by Gyan Bhanot (Rutgers Univer- a reception generously hosted by IPAM followed. sity, The Cancer Institute of New Jersey), Tom Chou On the second day, the first speaker, Joseph (UCLA, Mathematics), and Doron Levy (University Lehar (Novartis), discussed the role of cancer cell of Maryland, College Park) and was supported by lines in drug discovery and the identification of the National Science Foundation, UCLA and IPAM. synergistic combinations of existing drugs. Shridar The purpose of this workshop was to discuss cur- Ganesan (The Cancer Institute of New Jersey) dis- rent investigative directions in cancer research. The cussed the limitations of existing chemotherapeutic workshop brought together researchers from a va- treatments in targeting cancer cells, given the inter- riety of backgrounds, including medical doctors, bi- play between cell cycle dynamics and DNA repair ologists, physicists, mathematicians, and computer pathways. Monica Nicolau (Stanford) presented a scientists, to discuss aspects of cancer initiation, pro- framework for visualizing genetic changes in tumors gression, metastasis and treatment. It was fascinat- via topological clustering. In the afternoon, Eytan ing to compare the problems that each group was Domany (Weizmann Institute of Science) presented studying and how their approaches to these prob- an algorithm quantifying pathway deregulation lev- lems differed. The presentations given by clinicians els in individual tumors based on genetic expression were especially useful in identifying areas where data, in order to illuminate potential pathways as- mathematical modeling could be applied to better sociated with cancer survival. Trevor Graham (Barts understand a phenomenon. Cancer Institute) ended the second day of the work- shop with a discussion of carcinogenesis viewed as The first day of the workshop began with a pre- an evolutionary Darwinian process. He suggested sentation from Robert Gatenby (Moffitt Cancer Cen- that genetic diversity in tumors constitutes a univer- ter Research Institute), who emphasized that can- sal biomarker for cancer prognosis and progression. cer therapy should be adaptive and patient-specific. Moreover, rather than always choosing high-dosage therapy aimed at eradicating cancer, it may be ben- eficial to consider alternative drug schedules, for instance, administering the minimal effective dose that will maintain manageable levels of cancer. Beat- rice Knudsen (Cedars-Sinai) discussed the impor- tance of identifying good predictors in describing the pathology of a cancer, by using growth pat- terns, nuclear morphology, and immunohistochem- ical information to measure cancer severity in pa- tients. Linda Liau (UCLA) reported theoretical and empirical results on using immunotherapy in treat- ing glioblastomas, while Edwin Posadas (Cedars- Inna Brainis , Mingyang Lu, and Dana-Adriana Sinai) discussed the challenges in identifying molec- Botesteanu at the poster session ular classifiers and markers in diagnosing prostate

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 9 focused on epigenetic changes involved in cancer and the combination of epigenetic therapies with other standard techniques. Stefanie Jeffrey (Stan- ford) pointed out that it is frequently the spread of cancerous cells that leads to the demise of a patient, emphasizing the importance of studying circulating tumor cells as sources of metastatic growth and as prognostic signatures for early diagnosis of cancer recurrence. In the afternoon, Chang Chan (Rutgers) presented the Li-Fraumeni Syndrome, a genetic dis- order that causes significantly increased risk of sev- eral forms of cancer. A genetic regression model was proposed to explain the observation that aver- Prof. Eshel Ben-Jacob Lecturing on Exosomes and the age onset of cancer decreases across successive gen- Cancer-Immunity Cyberwar erations. Gabriela Alexe (Harvard) concluded the day’s talks with a discussion on metagene projection Wednesday began with two more presentations strategies as a tool for discovering functional anno- related to tumor initiation. Darryl Shibata (Uni- tations of genes and identifying synergistic changes versity of Southern California (USC)) introduced a at the micro and quantum levels derived from bi- framework for constructing a tumor’s ancestral tree ological data. The final day featured two presenta- based on the spatial distribution of mutations within tions, followed by an open-ended discussion of sev- it. Moreover, the distribution of mutations can be eral of the topics presented earlier in the week. First, used to distinguish between tumors with abnormal Kimryn Rathmell (UNC) described how genetic and cell motility, and therefore a high risk of invasion epigenetic data is used to further classify renal cell and metastasis, and benign tumors, that can po- carcinoma and distinguish it as a heterogeneous set tentially go untreated. Tibor Antal (Edinburgh) dis- of diseases. James Glazier (Indiana) concluded the cussed the application of multi-type branching pro- workshop with a presentation of a multi-scale multi- cesses in determining time to appearance of pas- cell computational modeling platform and its appli- senger mutations and the probability of tumor re- cation to age-related macular degeneration. lapse after initial therapy. The last morning presen- Lively discussions followed the many excellent tation, given by Hans Sieburg (Sanford-Burnham talks delivered throughout the week. Frequently, the Medical Research Institute), considered the clonal coffee breaks proved insufficient to conclude the diversity of hematopoietic stem cells and its implica- ongoing conversations. The diversity of the atten- tions regarding the mechanisms driving leukemias. dees’ backgrounds and experiences ensured a dy- In the afternoon, Eshel Ben-Jacob (Tel Aviv Univer- namic and engaging atmosphere, fostering cross- sity) introduced the concept of exosomes as pack- disciplinary connections at all levels. The warm and ages that facilitate long-distance communication be- welcoming atmosphere of IPAM was a definite cata- tween cells. He considered a mathematical model of lyst to these intellectually challenging conversations. cancer and immune cell competition that incorpo- The workshop provided an excellent opportunity rates exosomes. Benjamin Berman (USC) concluded for researchers in the physical and mathematical sci- the third day with a presentation of a new method ences and clinicians to form connections. Such ex- for analyzing epigenomic data, to identify changes periences represent a crucial step toward a more in- in epigenetic state across subpopulations of a tumor. tegrated approach to cancer research, where scien- On Thursday, Sui Huang (Institute for Sys- tists and clinicians collaborate regularly and influ- tems Biology) presented the concept of an epige- ence one another’s approaches. The number of re- netic landscape, where certain attractors represent searchers in attendance, and the diversity of institu- healthy development while others, which are not tions and locations throughout the world that they usually occupied by any cells, represent cancer. Ge- represented suggest that the scientific community is netic mutations or therapy can cause changes in the becoming more open to this cross-disciplinary form landscape that result in cells falling into cancer wells of research. More info at: http://www.ipam.ucla. or developing drug resistance. Peter Jones (USC) edu/programs/cdm2014/

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 10 SMB at the USA Science & Engineering Festival Thinking Like Ants! by ANDREW BASINSKI

The Science and Engineering Festival took place our participants were attracted to the booth upon this past April in Washington D.C. The massive event seeing the words “mathematical” and “biology” next attracted 325,000 people, and featured over 3000 to each other. The challenge was to pose questions hands-on activities for K-12 kids and their teachers. motivated by biology, but mathematical in nature, Space travel, 3D printing, and watershed manage- and make these questions accessible to an audi- ment were just a few of the panoply of topics repre- ence with a diverse background in both biology and sented. SMB’s booth showcased the fusion of mathe- math. Our booth used social insects (in particular, matics, computer simulation, and social insect ecol- ants) as a model organism in an attempt to make ogy. The diverse crowd of participants ranged from this idea intuitive and fun for kids and adults of all kindergartners attracted to bright colors, plastic ants ages. Participants were asked to think like an ant as and spinners, to high school teachers seeking new they played 3 boardgames demonstrating how ant ideas in relating the excitement and usefulness of colonies think, search their environment, and fight. math to their students. The most popular boardgame demonstrated how social insects, like proteins in a cell, collectively pro- duce complex behavior despite relatively simple in- dividual behaviors. The game was based off of the house-hunting ant Temnothorax - colonies of which collectively assess and choose a new nestsite after their current nest is destroyed. These ants have very particular preferences when choosing a new nest- site, and are able to collectively choose the best nest when given multiple options. This is incredible when paired with the fact that individual ants do not di- rectly compare nestsites. Instead, this comparison emerges as a result of two key individual behaviors: 1) ants that assess better nests communicate the po- tential nest location to more naive ants than those Raymond Mejia at the SMB booth in the Science and that visited lower quality nests; 2) ants spend a time Engineering Fair assessing the visited nestsite that is inversely pro- portional to its quality. Together, these individual be- Our goal was to show how math can be used to haviors favor the spread of information concerning understand complex biological processes. Readers of better nest options for the colony. this newsletter no doubt understand how math clar- We used boardgame-simulations to demonstrate ifies the mechanisms that allow cells to function, for this decentralized decision-making mechanism to example; however, it is easy to forget that the idea participants. Players spun spinners and guided plas- of combining math and biology is often downright tic ants through various petri dishes representing puzzling to the average student. Indeed, many of nests to directly observe how this decision-making

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 11 process takes place. Younger participants cheered and booed at the build-up of ants vying for the “good” and “bad” nestsites, while teachers com- mented on how such a game offers an interesting application in a course on statistics or dynamical systems. After playing the game, we discussed how math could be used to understand the influence of individual ants’ behavior on the colony’s ability to make the right decision. In another game, participants explored the re- lationship between searching efficiency and move- ment attributes of ants undergoing a random walk. Players rallied behind ants searching a checkerboard with 1 of 4 different random walks, and recorded the ability of the different ants to find baits (Hershey’s Andrew Basinski at the Science & Engineering Fair Kisses) distributed across the board. This game was extremely entertaining for groups of children, as well as for the people running the booth. After mov- ing several turns, kids were asked to hypothesize how the ability of finding food would differ for each type of ant, and what implications this has for real ants foraging their environment. Finally, a strategy game representing battles of the pavement ant, Tetramorium caespitum was built. Pavement ants are commonly seen on sidewalks in huge aggregations during territorial disputes of neighbors. To represent a colony-wide strategy dur- ing a dispute, players moved ants representing two neighboring colonies. At each turn, players chose to either advance their ants, or recruit ants to the bat- Preparation for the science festival involved the mass tlefront in a risk-like strategy game. Here, the ques- painting of plastic ants to be used in boardgame tion was how the outcome of a battle could be traced simulations. back to the fighting strategies of individual ants. The wealth of curiosity and wonder, especially of K-12 students, was absolutely inspiring. Interest- ingly, the most common reason people stopped at our booth was to ask how math and biology could possibly be studied together. Our focus was not in presenting mathematical models or solutions to bi- ological processes, but instead to give insight into the types of questions that demand mathematical modeling. Social insects provided a fun, insightful way to show youth how math is used to better un- derstand how complicated biological systems work.

For further information on The Science and En- gineering Festival check out their webpage: http: //www.usasciencefestival.org/2014-festival. html The finished product! These ants were used to simulate colony decision making, searching, and fighting

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 12 Computational Neuroscience Workshop McGill University, Montréal, April 29, 2014 by FRÉDÉRIC SIMARD,RICHARD GREG STACEY &LENNART HILBERT

Thursday April 29th was the second edition of hard work. One of last year’s speakers told us that our CAMBAM (Center for Applied Mathematics in he had been thanked by several people that had seen Bioscience And Medicine) student’s computational his video and he was happy to have given the talk. neuroscience workshop. For a second year, several Not only that, but he went as far as to include the graduate students have grouped together to offer a link to the video in his resume. Through this on- series of talks covering various tools and techniques line supplemental our workshop can offer continu- in computational neuroscience. ing benefits to both the speakers and future students This year, rather than chasing after speakers, we interested in the topics. were delighted to see many of last year’s speakers And finally, unlike several other seminars, we do come back. Given that this was a voluntary work- not measure the success of the event by counting shop and students have many competing interests, the number of participants, and in fact we’re biased we were happy to see people choose to return. More- toward keeping it small. As a student workshop, over, members of the audience from last year now we aimed to be as convivial as possible, and pro- wanted to give talks. This drive toward active par- vide a space where speakers and attendees merge ticipation didn’t limit itself to the speakers, as we together during the coffee breaks and everyone has observed a significant increase in the number of at- the time to express their thoughts and discuss their tendees, even though advertising for the event was opinions. During the workshop, beginners, inter- small. Our fears were eased. Because we see many mediates and experts all find the time to express seminars struggling to increase attendance we de- themselves and this is something we are not ready cided to share, through this newsletter, what we to sell out for the price of a few more attendees. think is our recipe for success. For more information, you can find a blog post of From the beginning our goal has been to create this year’s workshop by following the link here: an event that links students through a common fac- http://blogs.mcgill.ca/cambam/2014/04/07/ tor other than their research topics: computational computational-neuroscience-workshop-2014/ tools and techniques. We all do research in extraor- dinarily specialized topics, and often even our lab mates aren’t aware of what we’re really up to. When asked to participate in a local seminar, either as an attendee or a speaker, most of us know the slim chances that the topic will relate to our research. Our research questions are often too specific. To cor- rect this we took a different direction. Rather than speaking about their research projects, the speakers were asked to talk about their method of investiga- tion. How do I analyze my data? What kind of mod- els are available? What’s the appropriate stats test? Our workshop aimed to offer information about data analysis tools common to many research questions. From what we saw, interest in exchanging ideas about the fast-changing tools of the trade was very high. A second feature of our workshop is that each talk is shot and uploaded to YouTube. Speakers leave Frédéric Simard discussing the non-parametric aspects our event with something lasting that shows their of circular statistics.

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 13 Perspective on "New and Less New Opportunities For Mathematical Biology as Applied To Biological and Clinical Medicine" by JEAN CLAIRAMBAULT

Another conception that makes applications of mathematics quite different from applications of mathematics to sole biology resides in the interventionist nature of medicine ...

This perspective, bouncing from Philip Maini’s What had changed? Maybe the fact that biolog- "Perspective on The Changing Face of Mathematical Bi- ical phenomena that were until then considered as ology" 1, focuses on the specific case of mathematics just being there - the propagation of nerve impulse as applied to medicine. Philip Maini acknowledges or the spots on a leopard - were investigated by ad- the pioneering work of James D. Murray in Oxford: vanced scientists - physicists or mathematicians - as for sure, this immense founding enterprise with no having in fact a physical basis and hence a mathe- equivalent worldwide has led, through his stimulat- matical expression. Maybe in about the same way as ing teaching and research, to the training of scores in the Greek antiquity, presocratic philosophers and of students, from pure to very applied mathemati- the mathematicians among them tried to organize cians, many of whom have themselves become lead- a corpus of pre-existing observations (in particular ing scientists in different fields of mathematical bi- from Babylon and Egypt) according to rules, some ology. of which could be shown to be more than rules. In other parts of the world, such pioneers were The situation in which we are now is indeed scarce, but little by little, by the virtue of example, somewhat different. In a world where scientists of scientists coming either from the engineering world different disciplines regularly meet in conferences or from pure and applied mathematics learnt to and workshops, and publish jointly in journals in know that non-trivial mathematics had been written which attention is given to both mathematical mod- by some of them, starting from open biology ques- eling and experimental results, it is less likely that tions, often by transposing methods from physics breakthrough discoveries may be lost. Furthermore, or chemistry. For instance, reaction-diffusion equa- centers for mathematical biology, and as regards tions have been studied as providing a theoretical oncology, centers for integrated research on can- basis for traveling waves of physical phenomena by cer (essentially in the US for the latter) now ex- Kolmogorov, Petrovsky and Piskunov and indepen- ist and offer institutional opportunities to exchange dently by Fisher (for the spread of a gene in a pop- knowledge between disciplines, including mathe- ulation), all in 1937, and later a basis for morpho- matics and clinical medicine. In the UK, the Mathe- genesis by Turing in 1952. However, James Murray matics in Medicine Study Group (MMSG) organizes reports (Mathematical Biology 3rd ed., vol. 1, 13.2) meetings in different locations to model and tackle that the first discovery of the so-called KPP-Fisher during 2-3 days problems coming from requests by equation is due to the German chemist Luther in biologists or physicians. Even in places where such 1906, but also that his publication soon sank into institutions are not yet present, grants coming from oblivion, to be rediscovered later, much later than international and national calls more and more al- 1937. The scientific audience likely was not ripe low constituting coherent teams of applied mathe- then to catch the scope of this discovery and its maticians working in close contact with teams of bi- potential applications to biology, even though Fick ologists and - less frequently - physicians. (1855) in the same country had already presented As Philip Maini stresses, data coming from bi- his law of diffusion 50 years earlier. The now clas- ological experiments are most often static, i.e., sical examples of Hodgkin-Huxley (1952) and later snapshot-like, when we need movie-like data to FitzHugh-Nagumo models of action potential prop- identify the dynamics of the biological systems un- agation (1961, 1962) or Turing instability (1952) der study. Furthermore, a frequent and simplifying came later, on apparently more favorable ground. underlying assumption is that tissues are homoge- 1http://www.smb.org/publications/newsletter/vol27no1.pdf

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 14 neous, genetically and phenotypically, when for in- I see for the future, and it will make all the more stance multilocular samples in the same tumor show sense as the biological control mechanisms will be that this is frequently not the case, at least in can- more known. Even if they are not known in detail to cer. In biological and medical research teams, people perform quantitative predictions, qualitative results are keen on identifying intracellular signaling path- about optimized therapeutic strategies to combine ways - or cell membrane targets upstream of them drugs should prove helpful to clinicians. - searching for so-called “druggable targets" to block Of course, the continuous progress of imagery or enhance them. But the dynamic viewpoint that techniques, at all possible biological levels of ob- mathematicians are fond of "where does this lead to? servation, from intracellular signaling pathways to i.e., what is the asymptotic behavior of the system, whole-body recordings, in a more and more dy- controlled or not?", is seldom present. However, such namic way, i.e. with space and time resolutions that a dynamic perspective has always been present in are driving us from a scenery of poorly defined snap- the mind of biologists dealing with evolution, and shots to another one of high precision movies, will recently - remembering that, as stated by Theodo- never exclude the fact that important variables of sius Dobzhansky in 1973, “Nothing in biology makes the dynamic systems under study will remain hid- sense except in the light of evolution” - it has also be- den. This naturally calls for other new mathematical come clear at least for some cancer biologists. Some developments, which resort to statistical theory and indeed consider cancer as an evolutionary disease, to inverse problem methods. in the sense that cell populations evolve, partly with Such perspectives, some of them rather recent, prescribed rules, partly due to random events and together with a growing open-mindedness of biol- partly under the influence of tissue environmental ogists and physicians towards mathematics open factors, towards diseased states as populations of new tracks to follow for the growing number of multicellular organisms do. In my opinion, this view mathematicians interested in doing "mathematics for is about to deeply change our conception of diseases, medicine". There are hard problems - and less hard and in particular of cancer. ones - to solve, that will be a source of inspiration Another conception that makes applications of for mathematicians and a help to physicians - be it mathematics quite different from applications of only to provide new ways to ask questions - provided mathematics to sole biology resides in the interven- that the initial question is of biological and medical tionist nature of medicine, that is absolutely irre- nature, transposable in mathematical settings, and ducible to an applicative branch of biology. Whereas that a collaborative work is performed interactively the physicist describes the evolution with time of between members of the two disciplines towards natural phenomena, and in particular of diseases, advances in solving them. the physician is expected to correct them or prevent them, otherwise said to control them. This leads to About The Author: the idea, not only to apply optimization and opti- mal control principles to therapeutics, but also to Dr. Jean Clairambault, PhD, MD, design models of health and disease in tissues and trained - in that order - in mathe- organisms as dynamical systems under physiologi- matics and medicine, is presently cal control mechanisms that can be corrected when a senior scientist (“directeur de they fail. In this respect, firstly it is necessary to rein- recherche”) at INRIA and Labora- troduce physiology at the era of genetics at all levels toire Jacques-Louis Lions, Pierre where physiological regulations occur: intracellular et Marie Curie University in Paris. gene regulatory networks, equilibria between com- His current research interests are peting populations of cells, whole body hormonal the emergence of drug resis- regulations, and also between these levels; and sec- tance in cancer and the evolu- ondly, setting such physiological controls and the tion from premalignant cell populations to tu- correction of their disruptions as optimization prob- mors, together with therapeutic optimization meth- lems (physiologically solved or to be solved by thera- ods using combined drug delivery strategies to peutic intervention) should foster much more work overcome such evolutions at the cell population between physicians and mathematicians specialists level. Website: http://www.rocq.inria.fr/bang/ of optimal control. This is another opportunity that JC/Jean_Clairambault_en.html.

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 15 SMB Education Highlights New Guidelines for Programs in Mathematical Biology

by ELSA SCHAEFER

.. The report was intended to generate discussion and to address the challenges for mathematics departments of all shapes and sizes to create biology-inspired curricula for mathematics majors, ...

As many institutions are starting to consider the biological databases. the development or refinement of concentrations in The working group lists a basic set of mathemat- mathematical biology, our community has been ea- ical competencies that a concentration in biomath- ger to discuss best practices for these new programs, ematics should include, one that many mathemati- and to share ideas that make such program creation cians might largely duplicate without looking. They feasible for departments of varied sizes and research also include a list of biological competencies that a expectations. Perhaps all biomathematics programs biomathematics concentration could include, and I should include two key foundational courses that suspect that list may be a particularly helpful asset build competencies in modeling and in data anal- to mathematics programs interested in developing a ysis. A good program would also include a biomath- biomathematics concentration. ematics capstone course or undergraduate research The report was intended to generate discussion opportunity, something already offered by most de- and to address the challenges for mathematics de- partments. It is likely that other specific competen- partments of all shapes and sizes to create biology- cies needed for undergraduate students in math- inspired curricula for mathematics majors. The au- ematics can be fulfilled with courses already of- thors note that there has been much focus on and fered at most institutions, and thus new programs in success in establishing recommendations for a math- mathematical biology can be realistically established ematics curriculum for life sciences majors, but they at a wide variety of institutions. These are the main note that uniform recommendations for the incor- ideas presented in a thoughtful new report that was poration of biology into mathematics is likely in- unveiled at the 2014 Joint Mathematics meetings by appropriate given the tremendous diversity of the a working group serving on behalf of the commit- biomathematics field. tee on the Undergraduate Program in Mathematics (CUPM) of the Mathematical Association of Amer- The undergraduate mathematical biology report ica. outlines some of the challenges that face successful The first foundational biomathematics course program implementation, and its recommendations suggested by the working group focuses on the are intended to allow small departments to succeed importance of modeling and multiple mathemati- in creating such programs. One specific challenge for cal points of view (discrete, continuous, stochastic), biomathematics programs has been discussed in our including, of course, meaningful interaction with community for years: the institutional obstacles to the biological subject matter. The second suggested the hiring and support of truly interdisciplinary fac- foundational course would focus on data analysis, ulty, especially at non-research institutions. in particular, the ability to implement a statistical Other obstacles described are more typical of all comparison between data sets. This course should curricular efforts in mathematics, and perhaps the include regression analysis and fluency in at least most daunting concern for small programs is the po- one programming language, and an introduction to tential fragmentation of a small number of majors.

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 16 .. The mathematical biology guide provides a solid starting point for programs from multiple points of view without making the mistake of over-prescribing for this widely varied and emerging field, ...

The study group’s gentle and generic advice is 2014 CUPM reports can be accessed online at: for departments to start small - with modules in http://www2.kenyon.edu/Depts/Math/schumacherc/ existing courses, for example, and they addition- public_html/Professional/CUPM/Birds_feather. ally list resources to help faculty learn more about html#Programs biomathematics. The group was hesitant to pigeon- hole this broad field of biomathematics with specific About The Author: recommendations, and its report notes that there are Elsa Schaefer is a Pro- "many paths to success." Of course, collaboration be- fessor of Mathematics tween science and mathematics departments is ad- at Marymount Univer- vocated, and the report has some good suggestions sity. Her current re- about how to engage the administration and to en- search interests are courage their support of biomathematics efforts. in modeling disease The report also includes an institutional list of spread, and particu- contacts for biomathematics (listed by institution larly cholera and tick- type), as well as links to biomathematics resources borne diseases, and maintained by multiple societies and an impressive in seeking optimal in- list of textbooks that are now available. tervention strategies. The mathematical biology guide provides a solid She is past Secretary starting point for programs from multiple points of and current Electronic view without making the mistake of over-prescribing Communications Coordinator of the MAA’s BioSIG- for this widely varied and emerging field. This math- MAA, a red-dot and consultant for Project NExT, a ematical biology program report was one of multi- member of the MAA textbook committee, and the ple reports by Program Area Study Groups serving SMB Chair of Education. She was also the local on behalf of the committee on the Undergraduate organizer for the most recent BEER (Symposium Program in Mathematics (CUPM) of the Mathe- on Biomathematics and Ecology Education and Re- matical Association of America. The mathematical search) conference which was held at Marymount biology report was authored by Jennifer Galovich in October 2013, and she has served as a program (St. John’s University and chair of this committee), officer for the National Science Foundation’s Math- Fred Adler (University of Utah, SMB President), Lou ematical Biology program within the Division of Gross (University of Tennessee and Director of NIM- Mathematical Sciences. BioS), (Andrew Kerkhoff (Kenyon College), and Joe Her website: http://muweb.marymount.edu/ Mahaffy (San Diego State University). The January ~eschaefe/

In the next SMB Education column, I’d like to celebrate graduate school admission season with an overview of some PhD programs in mathematical biology. I’d like to share some modest information about the variety of programs available, and I am hoping to pull out some key program differences so that faculty in small programs like those being encouraged above can successfully steer our best students to the best-fitting program. I would love to hear from graduate directors about their advice to college seniors seeking further biomathematics studies. Please send me a note at [email protected].

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 17 "How The Leopard Gets Its Spots" the filling of a pail, but the lighting of a fire. The The Catalyst of My Mathematical day I heard Jim Murray speak sparked the fire for mathematical biology that has been burning in me Biology Journey! ever since. At that time, I did not understand much of the underlying theory that Jim presented, but I Trachette L. Jackson walked away from that seminar with the belief that mathematics could profoundly impact the biological and biomedical sciences. That day, I made a promise to myself that I would do everything in my power to eventually become one of Jim Murray’s students. Those were pretty big thoughts from a sheltered 20 year-old math major. It was, after all, rather late in my undergraduate training. It would be difficult for me to completely switch gears and embark on learn- ing a science that I was very unfamiliar with, while still trying to take a few graduate level mathematics courses that would help me get into a PhD program. So, I had a steep hill to climb. My first step was a Research Experience for Undergraduates (REU) with Professor Betty Tang, an Applied Mathemati- cian, working in mathematical biology, which led to my first publication. I also participated in the NIH- funded Minority Access to Research Careers (MARC) program, which gave me a crash course in biological research.

These experiences helped me to be admitted into the PhD program in Applied Mathematics at the Uni- versity of Washington and to achieve my goal of working under the direction of Jim Murray - the person who unknowingly started me on this path. Jim provided an atmosphere for his students that I "How The Leopard Gets Its Spots" flyers were pep- have never seen recreated. It was honestly the best pered all over the walls of the mathematics depart- possible place for me to learn to become a stew- ment at Arizona State University in the fall of 1992. ard of the discipline. My PhD thesis was based on They were advertising an upcoming lecture by Jim a problem presented to our Applied Math Clinic, Murray. I was an undergraduate mathematics major where researchers brought their scientific problems beginning my junior year of study in classical analy- to a group of motivated graduate students to work sis. I walked by this flyer every day for about a week on. At that time, considerable research was being and was simply perplexed as to why this lecture was aimed at improving the efficacy of chemotherapeu- being advertised in the Mathematics department. Fi- tic agents for cancer therapy. Dr. Peter Senter, a Bio- nally, I read a bit of the abstract, which said some- chemist working for Bristol Myers Squibb Pharma- thing about how a single mechanism could underlie ceutical Research Institute, was pioneering a promis- the wide variety of animal coat markings found in ing two-step approach designed to minimize sys- nature and that results from mathematical models temic drug toxicity while maximizing activity in tu- are opening lines of inquiry for developmental bi- mors by employing monoclonal antibody (mAb)- ologists. I had never been exposed to mathematical enzyme conjugates for the activation of anticancer efforts aimed at the biological sciences, so I decided prodrugs. Their research questions were ideal for to attend my first-ever departmental colloquium to mathematical modeling. By combining theory and hear Jim Murray speak. experiment, were able to quantify the biodistribu- William Butler Yeats said that education is not tion, pharmacokinetics and localization properties of

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 18 mAb-enzyme conjugates in tumor tissue and in the plexities associated with vascular tumor growth, in bloodstream. This was the first time I experienced the hopes of manipulating new knowledge for ther- the satisfaction and sense of accomplishment that apeutic gain. working at the interface of mathematics and biology As an educator, I have always been interested in now brings me everyday. My four years of gradu- the training and education of the next generation ate school, where I was able to work closely with of interdisciplinary mathematical scientists. There- experimentalists, taught me the power of collabora- fore, I quickly began developing courses and edu- tion and to communicate mathematics to biological cational experiences in Mathematical Biology when audiences. It also opened my eyes to the potential I arrived at the University of Michigan. Previously, for applied mathematics to become an integral part there had been no institutional mechanism for fac- of cancer research. ulty and students interested in quantitative methods When I earned my PhD in 1998, mathemati- in biology. To change this, Patrick Nelson and I co- cal biology was a booming and exciting field that founded the Mathematical Biology Research Group had gained international attention. Although I had a (MBRG) at the University of Michigan, which was tenure-track job offer, I decided that I needed time a campus wide initiative to foster interdisciplinary to explore and expand my research portfolio in order research at the interface of Mathematics and Biol- to become a productive and independent mathemat- ogy. We also developed the SUBMERGE (Supplying ical biologist. Fortuitously, the Institute for Mathe- Undergraduate Biology and Mathematics Education matics and Its Applications at the University of Min- and Research Group Experiences) program, which nesota was hosting its first annual thematic program aimed to merge the subjects of mathematics and bi- on Mathematics and Biology. I spent one amazing ology for undergraduate students by exposing them year there as a Postdoctoral Associate. Many of the to mentored, team-based research on real problems international leaders in Mathematical Biology - Lee in mathematical biology. Segal, Alan Perelson, Lisa Fauci, Zvia Agur and many Currently, I am coordinating a new Applied and others - rotated through the IMA that year, which Interdisciplinary Mathematics Bridge to the PhD gave me the opportunity to see the many different program at the University of Michigan in order to ad- configurations that a successful career could take. dress the national challenge of educating and train- My year at the IMA was an excellent introduc- ing a diverse scientific workforce capable of unify- tion to the worldwide community to which I wanted ing the fields of mathematics and the natural sci- to belong. I had the good fortune to share an of- ences. The program aims to impart on the next gen- fice with Helen Byrne, who took me under her wing eration of under-represented minority (URM) schol- and became a long-time mentor and collaborator. ars the foundational skills required to combine a The following year I moved to a second post-doc at deep knowledge of applied science with the mathe- Duke University. There I came to know Mike Reed matical, computational, and physical sophistication who, together with Jim Murray and Peter Senter, is needed to address the increasingly complex prob- one of the three greatest influences on my career as lems that are on the international horizon. a Mathematical Biologist. Mike facilitated research It is hard for me to believe that I have been in connections and collaborations and allowed me the this field for 16 years, but I know I would not be space to become an independent researcher. While where I am today if it were not for my biggest aca- at Duke, I was first introduced to the angiogenesis demic and research supporters, especially, Jim Mur- research that has been become a major emphasis in ray, Peter. Senter, and Mike Reed I met each of them my research program. at a different, yet critical, juncture in my career and During my first year at Duke, I applied to just have benefited greatly from knowing and working five places to test the waters for the potential of with them. After all this time, it still energizes me tenure-track positions. I accepted an offer from the to know that many of the various sub-disciplines of University of Michigan in the fall of 2000. To date, I mathematical biology are on the verge of critical sci- have had the opportunity to work with an outstand- entific advances. I am excited to see what the future ing group of collaborators, graduate students, and holds and am proud to call myself a Mathematical postdocs. Together, we have developed a variety of Biologist. cell-based and hybrid mathematical models of tumor Related Links: My home page: angiogenesis designed to untangle some of the com- http://www.math.lsa.umich.edu/ tjacks/

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 19 James D. Murray Talks About His Benter Prize

by JAMES D.MURRAY

To be awarded the 2012 William Benter Prize was a particular honor, which gave me enormous pleasure since it not only recognized applied mathematics as an important part of the mathematical sciences but also that it recognized the importance of our field of mathematical biology 2

Prizes in Mathematics and Mathematical Sci- ences universally mean pure mathematics irrespec- tive of the prize description. The William Benter Prize in Applied Mathematics, awarded every two years, is the first that I know of to single out Applied Mathematics. Bill Benter, who funded the prize, is, himself, a real applied mathematician whose practi- cal mathematical and computing skills are the ba- sis of his phenomenal betting business’ success in the Hong Kong horse racing market. Among other things, he supports a large number of charities. Professor Roderick Wong was responsible for the prize being associated with the City University of Hong Kong where the conferences are held. To be Prof. James D. Murray with Bill Benter and Prof. awarded the 2012 William Benter Prize was a par- Roderick Wong ticular honor, which gave me enormous pleasure since it, not only recognized applied mathematics as The atmosphere of the conference was incredi- an important part of the mathematical sciences but bly warm, friendly and welcoming and was among also that it recognized the importance of our field of the nicest I have ever been at. The warm atmosphere mathematical biology. was in large part due to the university administrator organizer Sophie Xi, and Roderick Wong. The meet- ing went without the slightest hitch with the student helpers genuinely helpful and very thoughtful. Those of us who started working in biologi- cal and medical applications many, many years ago came in for quite a lot of criticism and ridicule. When I decided that I did not want to do any more traditional applied mathematics research (in my case fluid dynamics) a colleague lectured me not to waste my time on "that rubbish". There were also lots of biologists who thought we could be of no use whatsoever but there were others, even in the early days, who were keen on interdisciplinary collabo- ration. Genuine interdisciplinary mathematics and biomedical research has been a pleasure to me prac- tically all my academic career. In the early days in the 1960s you could almost count those in the field Prof. James D. Murray delivering his lecture in one hand whereas now they number in the thou- following the Benter prize presentation ceremony sands with centers and societies all over the world. 2Read more about Prof. James D. Murray’s City U’s 2nd William Benter Prize: http://wikisites.cityu.edu.hk/sites/newscentre/en/Pages/201205281139.aspx

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 20 Oxford Mathematics Interviews: Jim Murray - Reflections on a Life in Academia

by PHILIP MAINI

Philip Maini interviewing Jim Murray

Jim Murray is one of the leading mathematical divorce. The Hooke lectures are part of a series of biologists of our times and the Inaugural Hooke Lec- Public Lectures intended to display the power and turer here in Oxford. In this wide-ranging interview beauty of mathematics to a wider audience. The lec- with Philip Maini, Professor of Mathematical Biol- ture attracted over 300 people and can be viewed at ogy in Oxford, Jim talks about his career, the range http://www.maths.ox.ac.uk/node/25270 of his work, his successes and failures and his hopes and expectations for a subject that is the pointing the way for the future of applied mathematics. Watch the full interview here: http://www.maths.ox.ac. uk/node/25330

Professor Jim Murray, gave the first Hooke Lec- ture here in Oxford on 4th March 2014, entitled "Why there are no 3-headed monsters, resolving some problems with brain tumors, divorce prediction and how to save marriages," Jim described three very different problems: the development of the mechan- ical theory of morphogenesis and how it was used to move evolution backwards; a model for quan- tifying the growth of brain tumors and individual patient treatments: and an example from the social sciences that is used to predict marital stability and Jim Murray Giving his Hooke Lecture at Oxford

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 21 Research Interview a biofilm infection. The bacteria within the biofilm are not genetically resistant to antibiotics, but the Beyond Boundaries biofilm provides several protective mechanisms. Un- derstanding why it is so difficult to kill the biofilms will help develop new treatment methods which has practical usefulness. Right now I am looking at biofilm-associated diseases within plants (specif- ically wine grape vines), bones, and in industrial filtration settings – all very important applications.

Why study bacterial dynamics and disinfection with applied mathematics? Why Not! It is cheaper than most experiments, more transparent (in that you can see things that are not visible to experi- mentalists), often more insightful than intuitive ex- periments can be. The connections that are made by applied mathematicians are often broader than are available to other scientists: mathematicians can see the similarities between forest fires and heart beats; bacterial swimming and soda pop bubbles; bacterial population dynamics and human disease Nick Cogan talks with Mark Whidden about his dynamics; etc. I think mathematical scientists are journey into mathematical biology and research on able to introduce lines of thought that experimen- biofilms talists/clinicians can use to jump start their research and, at the same time, help validate certain lines of Who or what inspired you to become a mathe- study. matical biologist? When I was an undergraduate I was fortunate to have a senior faculty member in the math department ask if I was interested in do- Which aspect of your research are you most ex- ing an honors thesis with him. At the time I knew cited about? I have been supervising numerous stu- that I wanted to do applied math, but I was thinking dents and one of the things that I am finding is more along the lines of working on some aspect of that they can lead me in directions that I would the space program. Dr. M. was collaborating with a not have moved myself. I have always believed that forensic scientist looking at ways to determine the one of the gaps in biofilm research, from a clini- time of death for a body that was exposed to the cal standpoint, is the lack of models that included elements for several weeks. We looked at a model of interaction between the biofilm pathogen and the insect dynamics for bugs that typically colonize car- host immune response. Even though there are many casses in the area. You can compare the predicted examples of the immune response to a bacterial life-stage populations with the observational data challenge, almost none are aimed at bacteria within and get a decent range for the time of death. I found a biofilm with all the multilayered protection that this a fascinating problem because it directly con- comes from the biofilm lifestyle. I really love that all nected mathematics to a practical need but with an of my current projects include direct collaboration interesting twist. with experimentalists or clinicians. I think that the interplay between the biology and the mathematics Tell us about your research. What are you work- is much more interesting and forward moving when ing on? My focus is on bacterial biofilms which are the biologist can help point to interesting questions aggregates of bacteria enmeshed in a self-produced that the mathematical analysis can shed light on. polymer gel that form very distinct structures. Biofilms are everywhere in natural, industrial, and What’s the next big thing in mathematical bi- medical environments. I am particularly interested ology? That is a big question – there are lots of in understanding why it is so difficult to eradicate things that need to be addressed. One part that I

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 22 am particularly keen on is how to understand the biologist and ask all the dumb questions that you role of uncertainty in the models. This means being can. able to quantify both the importance of particular parameters, but also some understanding of what What attracted you to a career in academia? Both uncertainty is inherent in the problem and what un- my parents were faculty members and I essentially certainty can be reduced by experimental data. This grew up on a college campus. It is an environment topic has been approached in other disciplines for where everyone was learning, discussing, arguing quite some time, but seems to be less well developed and generally being academics, and it feels like in mathematical biology. home. As I went to college and grad school I re- ally liked being around interesting people who were What are the most significant challenges you’ve interested in the world around them. Staying up late faced as an interdisciplinary scientist? As always, and talking about some particularly interesting topic I think it is the language gap between the mathe- was way more fun than putting on a suit and tie and matician and the experimentalists. It takes a lot of going to work. I also really like the freedom that time for the two research approaches (mathemati- comes in academia. cal versus experimental) to get on the same page. I think it used to be mainly the mathematicians job to How does your career influence your personal learn enough biology language to bridge the gap but life? I view myself as a scientist and I take my work I am finding that more and more experimentalists home with me. We homeschool our children and and data people are eager to learn the why and how they often ask leading questions. I encourage them of applied mathematics. Sometimes this is almost to look for answers on the own – experiment, ob- impossible, but the challenge is to make the mathe- serve, make bold hypotheses. Then look again in matics approachable so that, together, the team can a different way. Last year we collected data about find a common direction. whether toast really lands peanut butter side down – over the summer we will look at the descriptive Have you ever found the complexity of biological statistics and see what the answer is. The only down- systems daunting? Almost always – it is quite scary side is that I am never allowed to be right based on to move into a new area. There is so much to learn authority – I have to have some justification. and so much that you might be missing. Things like the immune system have been studied by so many If you were not a scientist, what would you be? really smart people – it is hard not to think that you Most likely a dishwasher. I used to work in kitchens can’t make a new contribution. But I know people before grad school and dishwashers have it pretty who feel that way about bacterial dynamics, which easy. Sometimes you get a freebie from a cook or I am more at home with. So I think it is a matter of bartender, you usually get your own music to listen time and effort. to, if you show up and do a decent job they think you are something amazing. Either that or a long- What would your message to a young and aspir- haul truck driver. ing mathematical biologist be? I think that there are so many aspects of biology that are not under- If you have any spare time, what do you do when stood and can be explored using mathematical tools. you are not working? My family travels quite a bit – However, it is not very clear what tools are most we are always up for a road trip to somewhere new. suited to an application. That means that, even more Mostly we just hang out and work on the house, than traditional applied mathematicians, mathemat- garden, and family life. ical biologists need to know a little bit about all sorts of mathematics. That way you can ask ques- About Nick G. Cogan tions about temporal dynamics, spatial dynamics, Dr. Nick Cogan is Associate Professor in the De- optimal control, topological constraints, special so- partment of Mathematics at Florida State University. lutions, perturbations, dynamical systems (discrete His research focuses on biofilm dynamics and host- and continuous), and on and on. You never know pathogen interactions. For more info, please visit: what tools will be useful, so stock up on as many http://www.math.fsu.edu/~cogan/ as possible. Also, whenever possible, find a friendly

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 23 The Future of What is your current research project? I am currently working on applications of patient- Mathematical Biology specific modeling in cancer. Generally speaking, I am interested in tailoring models to individual data Russell C. Rockne, Ph.D, Research Fellow through patient-specific (PS) parameter estimation. Department of Neurological Surgery at Ideally, these methods would only require data that Northwestern University is available as part of a patient’s medical care. Former PhD Student & Post-doc of Dr. Kristin Swanson What specific areas are you investigating? My dissertation work at the University of Washing- ton with my advisor Dr. Swanson focused on mod- eling the biological effects of radiation therapy with applications to glioblastoma brain tumors. I am con- tinuing to investigate patient-specific parameteriza- tions of growth and response models and the use of PS models in clinical research. I am also interested in using PS modeling to interpret the outcomes of clinical trials.

What do you hope to do after your postdoctoral work? I want to hold a research faculty position that is closely aligned with a clinical department. I want to develop scientific collaborations with clinicians to connect data-driven modeling to clinical research. To achieve this goal, I am applying for early career and training grants from the NIH–and some private funding agencies–that focus on clinical applications of PS modeling. These awards would support my transition to junior faculty.

What advice would you give to an undergraduate interested in a mathematical biology career? My advice would be to get a dual major in mathe- matics and another field, although not necessarily biology. You may not need a full bachelor’s degree What attracted you to mathematical biology? in biology to be successful in math bio. For exam- Mostly, I was curious about what kind of mathemat- ple, my research focuses on knowledge of cancer at ics would be required to describe biology. I quickly a clinical scale, which is different than the molec- realized that there is no master equation or sin- ular or cellular biology that might be the focus of gle technique for biology–how could there be? The an undergraduate degree. I would encourage tak- mathematics depends on the driving scientific hy- ing biology courses, but more generally to diversify pothesis, the biological situation, and the data. I your academic background. This will broaden your had my first research experience in math bio investi- toolset and inform your scientific creativity, which is gating a model for radiation therapy in glioblastoma an often overlooked skill. Personally, I pursued two brain tumors. I was a Master’s student working un- majors: mathematics and fine art. The further I get der the supervision of Dr. Kristin Swanson, whose into research, the more I appreciate the interplay mentorship and vision for how mathematics can be between my mathematical and artistic backgrounds. used to study cancer inspired me to pursue a Ph.D. and continue in research.

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 24 What inspires you scientifically? grown from essentially 1 staff scientist and a few I am inspired by the vision of mathematics as a tool students to 30 at its largest, composed of a diverse in an armamentarium for personalized medicine. mix of junior faculty, staff scientists, post-doctoral Imagine a future where doctors take measurements fellows, research techs, medical students, graduate and use quantitative principles and mathematical students and undergraduate students with the occa- models to make scientific decisions about which sional high school student. All the while Russ has treatment option would be best for you as a patient. served the role of "senior scientist." This is a big dream that might not happen in my ca- Russ is a natural leader while also accepting reer, but I am determined to contribute to advancing delegation of responsibilities with eagerness and fi- towards it. nesse. Russ’ growth as an independent thinker, sci- entist and senior manager has been exponential in Why did you join the Society for Mathematical preparation for an independent research role. Staff Biology? and peers alike frequently/often comment to me on I joined SMB because there is strength in numbers. how approachable and responsive Russ is for sci- As the society grows, so does the field and therefore entific discourse/parlance and educational needs as our future careers. Membership also has benefits: well as lab managerial issues. This reputation ex- student members are eligible for travel awards to tends to the broader scientific community of mathe- support their attendance at annual meetings of the maticians and clinicians alike who have already be- SMB, in addition to other SMB-sponsored work- gun to recognize Russ’ contributions to the field. Of shops and conferences. I have personally benefited particular note, data from Russ’ master thesis served from this support, as I recently received the Land- as preliminary data for our NIH R01 grant that ulti- hal travel award to participate in the SMB annual mately funded his PhD and his lab management (re- meeting in Arizona last year. I would like to take search scientist) position. In addition, Russ put forth this opportunity to thank the society for this support scientific propositions to further investigate tools for and for encouraging young scientists and graduate understanding radiation response to treatment. In students to take active roles in the society. I also summary, Russ is an excellent example of the bur- joined so I could help design t-shirts. ; ) geoning community of scientists truly at the scien- tific interface of mathematics and cancer who, I be- Dr. Kristin Swanson, Russell’s former lieve, will lead the field forward. PhD and Postdoctoral advisor, says:

I first met Russ in 2006 when I was looking for a master’s student for a research project. Amongst the plethora of applicants, Russ rose to the top. In short order he completed the research project and with it, his master’s thesis. Based on this incredi- ble work ethic, combined with his excellent research and managerial insights, I offered him a job as a research scientist and lab manager once he gradu- "The Future of Math Biology" is a column intended ated. His personality combined with his experience to highlight graduate students and postdoc in Math- teaching made him a perfect fit for my research ematical Biology. Do you want to nominate a stu- group which is heavily focused on mentorship and dent or a postdoc from your research group? Please student involvement. Russ has been instrumental in send your nomination to Amina Eladdadi: elad- the overall success of the lab through aiding the dadi(at)gmail.com growth of both staffing and science. The lab has

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 25 Positions Available tion of nutritional and metabolic systems (mecha- nistic and compartmental models, dynamical sys- tems with ODE, numerical analysis, parameter es- Master in Systems and Synthetic Biology: U timation and optimization). Interested applicants d’Evry-Val-d’Essonne. Online applications to the should email the following material to Helene Fouil- Master in Systems and Synthetic Biology (mSSB) are let ([email protected]) with subject open until 9 June 2014 (second round of applica- line "ModProtMetab Postdoc application": i) a cover tions). To find out more about mSSB, please visit our letter describing their background, research inter- website http://www.mssb.fr Applicants may come ests and motivation for the position, ii) a detailed from Universities or from Engineering schools af- CV with research experience, scientific and technical ter a first year of master (M1), or an equivalent skills, publication list and the contact information of qualification, in Life Sciences, Computer Sciences, at least two references, iii) copies of some of their Mathematics, Engineering, Chemistry and Physical best or most relevant papers. The starting date is ne- Sciences. Bi-disciplinary courses including Biology gotiable and the evaluation of candidates will begin is favored, but highly-achieving and motivated stu- immediately and continue until the position is filled. dents in any of the cited disciplines can apply. Fol- lowing this M2 Master, several PhD programs are Scientific Programmer/Researcher: CSDE, U possible on site. Research trainings are also pro- Washington. The University of Washington Cen- posed in Europe (England, Germany, Switzerland, ter for Studies in Demography and Ecology (CSDE) Spain) and in the US. and the UW Department of Microbiology invite ap- plications for a Scientific Programmer/Researcher PhD Positions: Basque Center for Applied Math- (Research Scientist/Engineer 3) to integrate within- ematics, Spain BCAM, the Basque Center for Ap- host models for viral dynamics into social net- plied Mathematics whose mission is to develop work models for the spread of HIV within popu- high quality interdisciplinary research in the fron- lations. To apply, go to https://uwhires.admin. tiers of Applied Mathematics, has opened an In- washington.edu/eng/candidates and enter req- ternational Call offering up to 7 PhD positions. uisition number 107046 in the required field. If Applications must be submitted on-line at: http: you have questions about this position, you may //www.bcamath.org/en/research/job Deadline for contact Josh Herbeck ([email protected]), Steve submission: June 2nd 2014, 17:00 CET Goodreau ([email protected]), or John Mittler ([email protected]). Post-doc: Ecology, U Federal de Vicosa, Brazil The Post-graduate Program in Ecology, at the Tenure Track in Mathematics: Risk Analysis, Umea Universidade Federal de Vicosa, in Vicosa, Mi- U, Sweden. We are seeking to fill a tenure-track posi- nas Gerais State, Brazil, is selecting a postdoc re- tion as associate senior lecturer in mathematics with searcher to join the Ecology Team of profession- specialization in risk analysis. The employment as als to work teaching and researching in Theoretical associate senior lecturer (bitradande universitetslek- Ecology, using mathematical modeling and compu- tor in Swedish) is permanent consisting of predomi- tational tools to investigate pattern and processes nantly research during the first four-year period, and structuring population and biological communi- with a possibility to build tutoring and pedagogi- ties. Other information about the scholarships for cal merits with up to 20% of the employment. At post-doctoral, can be found at: http://www.capes. the end of this employment period, an associate se- gov.br/images/stories/download/legislacao/ nior lecturer owns the right to be examined for a Portaria_86_2013_Regulamento_PNPD.pdf permanent position as senior lecturer at UmeNˇ Uni- versity. For further details and instructions on how Post-doc: Modeling Protein Metabolism, Paris. A to apply, see http://www8.umu.se/umu/aktuellt/ 2-year postdoc position in computational biology is arkiv/lediga_tjanster/2-534-14.html Your ap- available, in the domain of modeling and simula- plication should be received by May 28, 2014.

SMB Newsletter, MAY 2014, Volume 27, No 2 Page 26 Institute Events

dent training while fostering research at the inter- face of mathematics and biology. Visit http://www. nimbios.org/education/grad_fellowships

Upcoming Events & Opportunities at NIMBioS

Biology By Numbers, July 23-25: Apply now for the NIMBioS/BioQUEST Workshop: Biology by Numbers: Bringing Math to the High School Biology Emphasis Program for 2014-2015 is on Cancer Classroom, July 23-25, 2014, at NIMBioS. Applica- and Its Environment: tion deadline: June 6, 2014. Visit http://nimbios. org/tutorials/TT_curriculum_dev2014 Workshop 1: Ecology and Evolution of Cancer - September 15 - 19 Requests for Support, Sept. 1 : September 1 is Boot Camp: How to Simulate and Analyze Your the deadline for submitting proposals for new sci- Cancer Models with COPASI - September 29 - Oc- entific and educational activities at NIMBioS. Po- tober 01 tential organizers of activities in areas of molecu- Workshop 2: Metastasis and Angiogenesis - Oc- lar biology, cell biology, network biology, immunol- tober 13 - 17 ogy and systems biology are particularly encour- CTW: Axonal Transport and Neuronal Mechanics- aged to submit requests for support of Working November 03 - 07 Groups or Investigative Workshops. Visit http: Workshop 3: Cancer and the Immune System - //www.nimbios.org/research/ November 17 - 21 More info: Postdoctoral Fellowships, Sept. 1: September 1, http://mbi.osu.edu/programs/emphasis-programs/ 2014, is the next deadline for submitting appli- future-programs/cancer-and-its-environment-2014-2015/ cations for postdoctoral fellowships at NIMBioS. NIMBioS is particularly interested in requests to Editor’s Notes support research that integrates diverse fields, re- We invite submissions including summaries of pre- quires synthesis at multiple scales, and/or makes vious mathematical biology meetings, invitations use of or requires development of new mathe- to upcoming conferences, commentaries, book re- matical/computational approaches. Fellowships are views, or suggestions for other future columns. The for two years. Apply at http://www.nimbios.org/ deadline is the 15th of the month prior to publica- postdocs/ tion. The SMB Newsletter is published in January, May, Requests for Visits to NIMBioS: NIMBioS hosts and September by the Society for Mathematical short-term supported visitors and self-supported Biology for its members. The Society for Mathemat- visitors. Visit requests are considered at any time, ical Biology is an international society that exists but applications should be submitted a minimum to promote and foster interactions between the of 6 weeks prior to the proposed visit date. Visit mathematical and biological sciences communities http://nimbios.org/visitors/ through membership, journal publications, travel support and conferences. Please visit our website: Visiting Graduate Student Fellowship: NIMBioS http://www.smb.org for more information. offers fellowships for visits to NIMBioS for up to several months by graduate students interested in Editors: Holly Gaff & Amina Eladdadi email: pursuing research with NIMBioS senior personnel, editor(at)smb(dot)org postdoctoral fellows or working group participants. The program is designed to facilitate graduate stu- SMB Newsletter, MAY 2014, Volume 27, No 2 Page 27